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How to generate a .sif (simple interaction) file from gene micro array expression .tab file containing only gene expression values and gene names? I use Expander software and MeV and want to build an input file for Cytoscape and Spike software. Is there any R package or specific plugin or software for that purpose?

I can manually write .sif file based on precomputed correlation between genes:

CD31 pp CD34
BRCA pp CD31
VEGF pp CD34

However, don`t know how to generate it automatically using other metrics.

Thanks

LukDubMozaic
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Matthew Sprindzuk
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  • Could you post a sample of the .sif file you use to do manually the relation you posted? I am not used to these software. Also if your question is is there any X it is not under the guide of the site. Are you really trying to solve a programming problem ? – llrs Nov 09 '14 at 22:58
  • I need to build pathways from gene expression values. This is about data processing. Thanks. – Matthew Sprindzuk Nov 12 '14 at 17:37
  • Then we need some sample data to precess like you would like to show you how to do it. – llrs Nov 13 '14 at 10:41

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